The organization that makes the presidential transition guide said Monday that President Donald Trump's attorney took its manual out of context when he cited it to defend actions taken by the president's top advisors in the runup to Inauguration Day.

The lawyer, Ty Cobb, was quoted in a weekend report in The New York Times that documented close collaboration between senior members of Trump's transition team and retired Lt. Gen. Michael Flynn in the period when Flynn discussed U.S. sanctions with Russian Ambassador Sergey Kislyak.

"It would have been political malpractice not to discuss sanctions," Cobb said, according to the Times. "The presidential transition guide specifically encourages contact with and outreach to foreign dignitaries."

Cobb told CNBC that his quote in The New York Times was taken out of context in a way that changed its meaning. Cobb said that he meant that it would have been political malpractice not to discuss sanctions internally, among the transition staff. His reference to the presidential transition guide, he said, came much later in his interview with the Times.

The New York Times told CNBC on Monday, "Mr. Cobb was fairly and accurately quoted in our story."

But the notion that the transition guide encourages presidents-elect and their representatives to engage foreign leaders in policy talks stretches the intent of the guide, said Max Stier, president of the nonpartisan Partnership for Public Service, which compiled the guide.

"Our guide does not in any way, shape or form recommend that the president-elect get involved with foreign powers on policy issues," Stier told CNBC on Monday. "You can pull out language that there is going to be contact with foreign leaders, but that is not the intent of the guide."

The guide, which is available online, notes that calls to foreign officials are generally congratulatory and "typically do not touch heavily on outstanding policy issues."

"It is vital," the guide says, "that the president-elect and the staff understand the relevant protocol."

Cobb maintains that the Partnership for Public Service's 208-page guide blesses purposeful outreach.

"The presidential transition guide does specifically encourage outreach to foreign dignitaries, that's true. In fact, it encourages the transition team to build support and momentum for major policy initiatives," he told CNBC on Monday, citing a list of "action items" for the president-elect.

One of those action items, on page 179, reads: "Coordinate outreach to and interaction with major stakeholders — including foreign dignitaries, other branches of government and major political figures — to build support and momentum for major policy initiatives."

Stier, though, points to the second paragraph in that same chapter, which reads: "The incoming president's team should obey the maxim of 'one president at a time' and refrain from interfering with the policies of the incumbent. The transition team also should acknowledge and work with the outgoing administration to ensure the government is always speaking with one voice, especially on matters of national security and foreign policy."

"I think the guide is pretty clear that the basic principle is that there is one president," Stier told CNBC. "It can't be used legitimately as an excuse for a transition team to engage in conversations about foreign policy."

Flynn, who pleaded guilty on Friday to lying to the FBI, contacted Kislyak during the transition to request that the Kremlin not "escalate" tensions with the U.S., according to documents filed in federal court.

Flynn's request to the Russian government came the day after President Barack Obama announced sanctions on the country in retaliation for its meddling in the U.S. presidential election. According to court documents submitted by special counsel Robert Mueller, the Russian ambassador informed Flynn a few days later that, in response to Flynn's outreach, Russia decided not to ratchet up its retaliation against the United States.

The White House has said that Flynn's contacts with the Russian ambassador during the transition were lawful and that his false statements to federal investigators were "a shame."

The Partnership for Public Service's Center for Presidential Transition advised Trump's transition team and provided copy that was used on its website. Stier said the group did not discuss communications between transition officials and the Russian government.